@datagrok/helm 2.1.1 → 2.1.2

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.1",
+  "version": "2.1.2",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
   },
   "description": "",
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.15.1",
+    "@datagrok-libraries/bio": "^5.21.0",
     "@datagrok-libraries/utils": "^1.19.1",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.11.1",
@@ -23,12 +23,8 @@
     "helm/JSDraw/Pistoia.HELM-uncompressed.js"
   ],
   "devDependencies": {
-    "@types/jest": "^27.0.0",
-    "jest": "^27.0.0",
-    "jest-html-reporter": "^3.6.0",
     "path": "^0.12.7",
     "puppeteer": "^13.7.0",
-    "ts-jest": "^27.0.0",
     "ts-loader": "^9.2.6",
     "typescript": "^4.4.4",
     "webpack": "^5.59.1",
@@ -56,9 +52,9 @@
     "release-helm-public": "grok publish public --release",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix",
-    "test": "jest",
-    "test-dev": "set HOST=dev && jest",
-    "test-local": "set HOST=localhost && jest"
+    "test": "grok test",
+    "test-dev": "grok test --host dev",
+    "test-local": "grok test --host localhost"
   },
   "canEdit": [
     "Developers"

package/src/cell-renderer.ts

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {findMonomers, parseHelm, getParts} from './utils';
-import {printLeftOrCentered} from '@datagrok-libraries/bio';
+import {printLeftOrCentered} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
 
 export class HelmCellRenderer extends DG.GridCellRenderer {
@@ -50,7 +50,7 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
       if (monomers.has(allParts[i]))
         tooltipMessage[i] = ui.divV([
           ui.divText(`Monomer ${allParts[i]} not found.`),
-          ui.divText('Open the Property Panel, then expand Manage Libraries')
+          ui.divText('Open the Context Panel, then expand Manage Libraries')
         ]);
     }
     (((tooltipMessage[left]?.childNodes.length ?? 0) > 0))

package/src/package.ts

@@ -5,8 +5,9 @@ import * as DG from 'datagrok-api/dg';
 
 import {WebEditorMonomer, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
 import {HelmWebEditor} from './helm-web-editor';
-import {NotationConverter, IMonomerLib, Monomer} from '@datagrok-libraries/bio';
 import {HelmCellRenderer} from './cell-renderer';
+import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
 
 export const _package = new DG.Package();
 let monomerLib: IMonomerLib | null = null;

package/jest.config.js

@@ -1,34 +0,0 @@
-module.exports = {
-  "roots": [
-    "<rootDir>/src"
-  ],
-  "testMatch": [
-    "**/__jest__/**/*.test.+(ts|tsx)"
-  ],
-  moduleFileExtensions: [
-    'ts',
-    'js',
-  ],
-  "transform": {
-    "^.+\\.(ts|tsx)$": "ts-jest"
-  },
-  transformIgnorePatterns: ['^.+\\.js$'],
-  globals: {
-    'ts-jest': {
-      'tsconfig': {
-          "target": "es6",
-          "module": "es2020",
-      }
-    }
-  },
-  reporters: [
-    "default",
-    [
-      "./node_modules/jest-html-reporter",
-      {
-        "includeConsoleLog": true,
-        "includeFailureMsg": true
-      }
-    ]
-  ]
-}

package/src/__jest__/remote.test.ts

@@ -1,77 +0,0 @@
-/**
- * @jest-environment jsdom
- */
-
-import * as utils from './test-node';
-import puppeteer from 'puppeteer';
-
-const P_START_TIMEOUT: number = 3600000;
-let browser: puppeteer.Browser;
-let page: puppeteer.Page;
-
-beforeAll(async () => {
-  let out = await utils.getBrowserPage(puppeteer);
-  browser = out.browser;
-  page = out.page;
-}, P_START_TIMEOUT);
-
-afterAll(async () => {
-  await browser?.close();
-});
-
-expect.extend({
-  checkOutput(received, expected, context) {
-    if (received === expected) {
-      return {
-        message: () => context,
-        pass: true
-      };
-    } else {
-      return {
-        message: () => context,
-        pass: false
-      };
-    }
-  }
-});
-
-it('TEST', async () => {
-  const targetPackage:string = process.env.TARGET_PACKAGE ?? 'Helm';
-  console.log(`Testing ${targetPackage} package`);
-
-  let r = await page.evaluate((targetPackage):Promise<object> => {
-    return new Promise<object>((resolve, reject) => {
-      (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
-        const cStatus = df.columns.byName('success');
-        const cSkipped = df.columns.byName('skipped');
-        const cMessage = df.columns.byName('result');
-        const cCat = df.columns.byName('category');
-        const cName = df.columns.byName('name');
-        const cTime = df.columns.byName('ms');
-        let failed = false;
-        let skipReport = '';
-        let passReport = '';
-        let failReport = '';
-        for (let i = 0; i < df.rowCount; i++) {
-          if (cStatus.get(i)) {
-            if (cSkipped.get(i)) {
-              skipReport += `Test result : Skipped : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-            } else {
-              passReport += `Test result : Success : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-            }
-          } else {
-            failed = true;
-            failReport += `Test result : Failed : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-          }
-        }
-        resolve({failReport, skipReport, passReport, failed});
-      }).catch((e: any) => reject(e));
-    });
-  }, targetPackage);
-  // @ts-ignore
-  console.log(r.passReport);
-  // @ts-ignore
-  console.log(r.skipReport);
-  // @ts-ignore
-  expect(r.failed).checkOutput(false, r.failReport);
-}, 7200000);

package/src/__jest__/test-node.ts

@@ -1,96 +0,0 @@
-import * as path from "path";
-import * as os from "os";
-import * as fs from "fs";
-import * as yaml from 'js-yaml';
-import fetch from 'node-fetch';
-
-export async function getToken(url: string, key: string) {
-  let response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
-  let json = await response.json() as Record<string, any>;
-  if (json.isSuccess == true)
-    return json.token;
-  else
-    throw 'Unable to login to server. Check your dev key';
-}
-
-export async function getWebUrl(url: string, token: string) {
-  let response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
-  let json = await response.json() as Record<string, any>;
-  return json.settings.webRoot;
-}
-
-const grokDir = path.join(os.homedir(), '.grok');
-const confPath = path.join(grokDir, 'config.yaml');
-
-function mapURL(conf: Config): Indexable {
-  let urls: Indexable = {};
-  for (let server in conf.servers) {
-    urls[conf['servers'][server]['url']] = conf['servers'][server];
-  }
-  return urls;
-}
-
-export function getDevKey(hostKey: string): {url: string, key: string} {
-  let config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
-  let host = hostKey == '' ? config.default : hostKey;
-  host = host.trim();
-  let urls = mapURL(config);
-  let key = '';
-  let url = '';
-  try {
-    let url = new URL(host).href;
-    if (url.endsWith('/')) url = url.slice(0, -1);
-    if (url in urls) key = config['servers'][urls[url]]['key'];
-  } catch (error) {
-    if (config['servers'][host] == null)
-      throw `Unknown server alias. Please add it to ${confPath}`;
-    url = config['servers'][host]['url'];
-    key = config['servers'][host]['key'];
-  }
-  return {url, key};
-}
-
-export async function getBrowserPage(puppeteer: any): Promise<{browser: any, page: any}> {
-  let url:string = process.env.HOST ?? '';
-  let cfg = getDevKey(url);
-  url = cfg.url;
-
-  let key = cfg.key;
-  let token = await getToken(url, key);
-  url = await getWebUrl(url, token);
-  console.log(`Using web root: ${url}`);
-
-  let browser = await puppeteer.launch({
-    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
-    ignoreHTTPSErrors: true,
-  });
-
-  let page = await browser.newPage();
-  await page.setDefaultNavigationTimeout(0);
-  await page.goto(`${url}/oauth/`);
-  await page.setCookie({name: 'auth', value: token});
-  await page.evaluate((token: any) => {
-    window.localStorage.setItem('auth', token);
-  }, token);
-  await page.goto(url);
-  try {
-//    await page.waitForSelector('.grok-preloader', { timeout: 1800000 });
-    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 3600000});
-  } catch (error) {
-    throw error;
-  }
-  return {browser, page};
-}
-
-
-interface Config {
-  servers: {
-    [alias: string]: {
-      url: string,
-      key: string
-    }
-  },
-  default: string,
-}
-
-interface Indexable { [key: string]: any }

package/test-Helm-c4a2a41b7b00-07e4a533.html

@@ -1,249 +0,0 @@
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-.suite-container {
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Helm Test Report. Datagrok version datagrok/datagrok:bleeding-edge SHA=c4a2a41b7b00. Commit 07e4a533.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2023-01-05 12:03:23</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts</div><div class="suite-time warn">13.336s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">2.808s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:61:11)
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:40:11
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:34:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:30:12)
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:38:23)
-    at Promise.then.completed (/home/runner/work/public/public/packages/Helm/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Helm package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:72:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 20 : Helm.Helm.parseHelm : OK
-</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:74:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>